.sdf of only clusters leads

[eneas77]

Hi,

After working for so long with AD4/AD-GPU, i appreciate the possibility Meeko brings of transforming the dreadful .dlg files into .sdf
However, it is pretty much a dead end if the clustering information is not exported as well in some way...

A more appealing alternative would be to retrieve the sdf of only clusters leads, together with full energetic terms, cluster population and docking run number.

Hope it inspires you...

E77

[diogomart]

A tiny piece of this - storing some of the energies - has been implemented meanwhile. We didn't yet implement getting only the cluster leads. But I agree it is inspiring... :-)

from rdkit import Chem
import json

for mol in Chem.SDMolSupplier("docked.sdf"):
    data = json.loads(mol.GetProp("meeko"))
    print(data)

{'free_energy': -6.663, 'intermolecular_energy': -7.154, 'internal_energy': -2.099}
{'free_energy': -6.566, 'intermolecular_energy': -7.048, 'internal_energy': -2.099}
{'free_energy': -6.4, 'intermolecular_energy': -7.401, 'internal_energy': -1.566}
{'free_energy': -6.177, 'intermolecular_energy': -7.189, 'internal_energy': -1.536}
{'free_energy': -5.977, 'intermolecular_energy': -6.506, 'internal_energy': -2.001}

[diogomart]

Exporting an SDF of only cluster leads implemented in 27938b3

[diogomart]

Forgot to expose the option in the command line script mk_export.py, option is -c or --only_cluster_leads.
Commit: 439ebee